SeqTrim is a pipeline designed to preprocessing sequence reads. It is easy to install and configure, flexible even if default parameters are accurate for most purposes and usable as a web interface or a standalone command line application. It identifies the sequence insert by removing low quality sequences, cloning vector, poly-A or poly-T tails, adaptors and any contaminant sequence or unwanted feature. Several input and output formats are available, which enables its inclusion in already or newly defined sequence processing work flows. It outperforms preprocessors implemented in other web servers and standalone applications at least in detecting adaptors and chimeric clones. SeqTrim is under continuous refinement to deal with most sequence events due to collaboration between biologists and computer scientists. SeqTrim07: a pipeline for preprocessing sequence reads Málaga University. His research interests include issues related to user interfaces and formal design. He has published a great number of articles at international journals, conference proceedings, book chapters, as well as open source software. Antonio J. Lara is a PhD student developing new tools for sequence analysis. He has published a great number of articles at international journals, conference proceedings, book chapters, as well as open source software. Guillermo Pérez-Trabado is a Professor of Computer Architecture at Málaga University. His research interests are related to parallelisation of processes and integration of databases with algorithms for bioinformatics. He has published a great number of articles at international journals, conference proceedings, book chapters, as well as open source software. Noé Fernández-Pozo is a PhD student testing new tools for sequence analysis. Francisco R. Cantón is a Professor of Biochemistry and Molecular Biology at Málaga University. His research interests include issues of expression analysis of genes related to wood synthesis in conifers. He has published a great number of articles at international journals, conference proceedings, book chapters, as well as open source software. M. Gonzalo Claros is a Professor of Molecular Biology at Málaga University. His research interests are related to automated high-throughput analysis of gene expression data. He has published a great number of articles at international journals, conference proceedings, book chapters, as well as open source software.